Robert J. Kleberg, Jr. and Helen C. Kleberg Foundation

Spermatogenesis is driven by dramatic changes in chromatin regulation, gene transcription, and protein expression. To assess the mechanistic bases for these developmental changes, we utilized multiomic single-cell/nucleus RNA sequencing (sc/snRNA-seq) and single-nucleus assay for transposase-accessible chromatin with sequencing (snATAC-seq) to identify chromatin changes associated with transcription in adult mouse and rat testes. We characterized the relationships between the transcriptomes and chromatin of both species, including the divergent expression of Id4 in spermatogonial stem cells between species. Promoter accessibility and gene expression showed the greatest association during meiosis in both species. We mapped the cross-species conservation of putative regulatory regions for key spermatogenic genes, including Cd9 and Spam1, and investigated correlations and disconnects in chromatin accessibility, gene expression, and protein expression via antibody-derived tags. Using a gene regulatory network (GRN) model, we identified 40 core regulons conserved between mouse and rat germ cells, highlighting the relevance of chromatin-related factors in regulating the transcription of canonical genes across spermatogenesis.

Eoin C. Whelan^1,10 ewhelan@vet.upenn.edu ∙ John J. Swain^1,2,6,8 ∙ Jonathan H. Sussman^3,4,5,8 ∙ David Smith³ ∙ Fan Yang^1,7 ∙ Antonia Rotolo² ∙ Mary R. Avarbock¹ ∙ Clara Malekshahi² ∙ Enrico Radaelli² ∙ Daniel P. Beiting² ∙ Ralph L. Brinster^1,9

Stem Cell Reports Volume 20, Issue 4, 102449April 08, 2025

https://doi.org/10.1016/j.stemcr.2025.102449